Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021585.1 Corchorus olitorius cultivar O-4 contig21618, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 44546
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:91 original size:6 final size:7
Alignment explanation
Indices: 74--98 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
64 TTTCAAGAGG
74 GGGGGGT
1 GGGGGGT
81 GGGGGGT
1 GGGGGGT
88 GGGGGGT
1 GGGGGGT
95 GGGG
1 GGGG
99 AGGGAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.88, T:0.12
Consensus pattern (7 bp):
GGGGGGT
Found at i:310 original size:22 final size:20
Alignment explanation
Indices: 279--385 Score: 65
Period size: 22 Copynumber: 5.0 Consensus size: 20
269 TGCGCTTACC
*
279 AATTTTATAGTGTGATTATCAA
1 AATTTCATAG-GTG-TTATCAA
*
301 AATTTCATAGGAAGATTATCAA
1 AATTTCATAGG-TG-TTATCAA
*
323 AATTTCACAGAGTGGTTATCAA
1 AATTTCATAG-GT-GTTATCAA
** *
345 GTTTTCATA-G-GTTATCGA
1 AATTTCATAGGTGTTATCAA
*
363 AATTTCATAATGATGTTATCAA
1 AATTTCAT-A-GGTGTTATCAA
385 A
1 A
386 CACATTATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
18 13 0.20
19 1 0.02
20 1 0.02
21 1 0.02
22 48 0.73
23 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (20 bp):
AATTTCATAGGTGTTATCAA
Found at i:2280 original size:90 final size:89
Alignment explanation
Indices: 2177--2346 Score: 270
Period size: 90 Copynumber: 1.9 Consensus size: 89
2167 TTACTATGTA
** *
2177 ATAATTATTTGAACAGTTACCTAATT-AAAGGATTTAGGAAGTTATTCATTTTGAATAAAAAACA
1 ATAATTACCTGAACAGTTACCTAATTAAAAGGA-TTAGAAAGTTATTCATTTTGAAT-AAAAACA
2241 ATTTATTGATTTGATAATTGTTCAAG
64 ATTTATTGATTTGATAATTGTTCAAG
* *
2267 ATAATTACCTGAACAGTTACCTAATTAAAAGGATTAGAAAGTTATTCATTTTGAATAATAACAGT
1 ATAATTACCTGAACAGTTACCTAATTAAAAGGATTAGAAAGTTATTCATTTTGAATAAAAACAAT
2332 TTATTGATTTGATAA
66 TTATTGATTTGATAA
2347 CCGTTTAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 22 0.30
90 46 0.62
91 6 0.08
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (89 bp):
ATAATTACCTGAACAGTTACCTAATTAAAAGGATTAGAAAGTTATTCATTTTGAATAAAAACAAT
TTATTGATTTGATAATTGTTCAAG
Found at i:3875 original size:69 final size:69
Alignment explanation
Indices: 3761--3890 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 69
3751 AAATCTTAGG
* *
3761 TCTCTCTCGCAATCAATTTTCTGGGAATATTTCTGTCCTTCAGAGTCTAACATCCCTCCAAAGTG
1 TCTCTCTCGCAATCAATTTTCTGGGAATATATCTGCCCTTCAGAGTCTAACATCCCTCCAAAGTG
3826 TAGA
66 TAGA
* * * * *
3830 TCTCTCTTC-CAATCAGTTTT-TTGGAGATATATCTGCCCTTGAGAGTTTGACATCCCTCCAA
1 TCTCTC-TCGCAATCAATTTTCTGGGA-ATATATCTGCCCTTCAGAGTCTAACATCCCTCCAA
3891 TATCTGAGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 4 0.08
69 46 0.88
70 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (69 bp):
TCTCTCTCGCAATCAATTTTCTGGGAATATATCTGCCCTTCAGAGTCTAACATCCCTCCAAAGTG
TAGA
Found at i:7486 original size:29 final size:29
Alignment explanation
Indices: 7453--7513 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
7443 CCAATAAAAT
*
7453 ATTTTGTTTTATTAGTC-AAAACAGGGATG
1 ATTTT-TTTTATTAGCCAAAAACAGGGATG
* *
7482 ATTTTTTTTTTTGGCCAAAAACAGGGATG
1 ATTTTTTTTATTAGCCAAAAACAGGGATG
7511 ATT
1 ATT
7514 CTATTCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (29 bp):
ATTTTTTTTATTAGCCAAAAACAGGGATG
Found at i:26054 original size:24 final size:24
Alignment explanation
Indices: 26027--26082 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
26017 AAGAAAAGTA
26027 AGAAGAAGAGCAAT-AAGGCTGAAG
1 AGAAGAAGAGCAATGAA-GCTGAAG
* *
26051 AGAACAAGAGCAGTGAAGCTGAAG
1 AGAAGAAGAGCAATGAAGCTGAAG
26075 AGAAGAAG
1 AGAAGAAG
26083 GCGGTGGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (24 bp):
AGAAGAAGAGCAATGAAGCTGAAG
Found at i:26120 original size:60 final size:60
Alignment explanation
Indices: 26051--26278 Score: 348
Period size: 60 Copynumber: 3.8 Consensus size: 60
26041 AAGGCTGAAG
* * * * * *
26051 AGAACAAGAGCAGTGAAGCTGAAGAGAAGAAGGCGGTGGACCAAATTGAGGAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
*
26111 AGAAGAAGAGCAATGAAGCTGAAGGGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
* * **
26171 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTATGGACCAGATTGACAAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
*
26231 AGAAGAAGAGCAAAAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTG
1 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTG
26279 TGGACAAGAA
Statistics
Matches: 155, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 155 1.00
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.10
Consensus pattern (60 bp):
AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
Found at i:29928 original size:4 final size:4
Alignment explanation
Indices: 29919--29959 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
29909 CTTTAAACAA
*
29919 AAAG AAAG AAAG AAAG AAAG AAAG AAA- AAAA AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
29960 GAAGAAGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:44509 original size:2 final size:2
Alignment explanation
Indices: 44502--44542 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
44492 ACAAGTAATT
44502 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
44543 GAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.